Gene content array of <i>Rickettsia</i> plasmidome obtained from BBH analysis.

<p>The right three columns showed the pRIG references of putative ortholog gene groups, the total number of genes for each pRIG and its corresponding annotation including its COGID form COG database. Each member of the pRIG was annotated as either complete (red), split (yellow), fragment (blue), chimeric (green) and absent (or remnant, violet).</p

<i>Rickettsia</i> and <i>Orientia</i> genomes extracted from the National Center for Biotechnology Information (NCBI) database.

<p><i>Rickettsia</i> and <i>Orientia</i> genomes extracted from the National Center for Biotechnology Information (NCBI) database.</p

Evolutionary scenario of rickettsial plasmids.

<p>Evolutionary scenario of rickettsial plasmids.</p

Frequencies of complete and degraded (split, fragment or chimeric) genes identified in the plasmidome of <i>Rickettsia</i>.

<p>Frequencies of complete and degraded (split, fragment or chimeric) genes identified in the plasmidome of <i>Rickettsia</i>.</p

COG functional categories of <i>Rickettsia</i> plasmidome originated from vertical and horizontal evolutions as well as duplications.

<p>COG functional categories of <i>Rickettsia</i> plasmidome originated from vertical and horizontal evolutions as well as duplications.</p

Supertree obtained from 10 genes of <i>Rickettsia</i> plasmids as well as <i>Rickettsia</i> and <i>Orientia</i> chromosomes using subtree prune-and-regraft distance (D = 64).

<p><i>Candidatus Midichloria mitochondrii</i> (YP_004679220.1) and <i>Pantoea ananatis</i> (YP_005193440.1) were used as outgroups. The list of genes used are two transposases, patatin-like phospholipase, thymidylate kinase, heat shock protein, <i>dna</i>A-like replication initiator proteins, helix-turn-helix DNA-binding domain, cell surface antigen Sca12, conjugative transfer protein containing <i>tra</i>D domain, and leucine rich-repeat containing protein. In the right, summary of evolutionary events that shaped rickettsial plasmids.</p

Rickettsial plasmid sizes (pooled) and numbers plotted with their chromosome sizes.

<p>Rickettsial plasmid sizes (pooled) and numbers plotted with their chromosome sizes.</p

Examples of EPIMIC stool samples and rotavirus diagnoses surveillance tables and plots.

<p>Table (A) shows counts of stool samples and positive diagnoses of rotavirus entered each week into an EPIMIC Microsoft Excel file; numbers in red font are those above the alert threshold corresponding to the mean plus 2 standard deviations calculated for historical data and shown in the top rows of the table. Plots B, C and D show cumulated weekly numbers of stool samples received at our laboratory, of positive rotavirus diagnosis, along with the proportions of positive samples per season (B), year (C) and month (D). Nb, number.</p

EPIMIC organization chart.

<p>Groups of items currently surveyed by EPIMIC, classified according to infectious syndromes or platforms based on specific technologies or dedicated to specific pathogens. See also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144178#pone.0144178.s003" target="_blank">S3 Table</a>.</p

EPIMIC methicillin-resistant <i>Staphylococcus aureus</i> surveillance plot.

<p>The purple envelope represents the 95% confidence interval of the blue slope.</p